High-throughput fingerprinting of bacterial artificial chromosomes using the snapshot labeling kit and sizing of restriction fragments by capillary electrophoresis

Luo, Ming‐Cheng; Thomas, Carolyn; You, Frank M.; Hsiao, Joseph; Ouyang, Shuai; Buell, C. Robin; Malandro, Marc S.; McGuire, Patrick E.; Anderson, Olin D.; Dvořák, Jan

doi:10.1016/s0888-7543(03)00128-9

Cited by 235 publications

(260 citation statements)

References 14 publications

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“…Morex by high-information-content fingerprinting 7 and contig assembly 8 of 571,000 bacterial artificial chromosome (BAC) clones (,14-fold haploid genome coverage) originating from six independent BAC libraries 9 . After automated assembly and manual curation, the physical map comprised 9,265 BAC contigs with an estimated N50 contig size of 904 kilobases and a cumulative length of 4.98 Gb (Methods, Supplementary Note 2).…”

Section: A Sequence-enriched Barley Physical Mapmentioning

confidence: 99%

A physical, genetic and functional sequence assembly of the barley genome

2012

Nature

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Barley (Hordeum vulgare L.) is among the world's earliest domesticated and most important crop plants. It is diploid with a large haploid genome of 5.1 gigabases (Gb). Here we present an integrated and ordered physical, genetic and functional sequence resource that describes the barley gene-space in a structured whole-genome context. We developed a physical map of 4.98 Gb, with more than 3.90 Gb anchored to a high-resolution genetic map. Projecting a deep whole-genome shotgun assembly, complementary DNA and deep RNA sequence data onto this framework supports 79,379 transcript clusters, including 26,159 'high-confidence' genes with homology support from other plant genomes. Abundant alternative splicing, premature termination codons and novel transcriptionally active regions suggest that post-transcriptional processing forms an important regulatory layer. Survey sequences from diverse accessions reveal a landscape of extensive single-nucleotide variation. Our data provide a platform for both genome-assisted research and enabling contemporary crop improvement

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Section: A Sequence-enriched Barley Physical Mapmentioning

confidence: 99%

A physical, genetic and functional sequence assembly of the barley genome

2012

Nature

1,285

880

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“…This effort will entail fingerprinting approaches that capture the maximum information possible in each lane (e.g. HICF or SNAPshot; Ding et al, 2001;Luo et al, 2003), and must be conducted in concert with a communitydriven effort to resolve contig ambiguities associated with duplicated segments of the genome and to anchor the physical map to the genetic map. Generation of BAC-end sequences from the BACs making up the physical map will provide for the placement of hundreds of ESTs, will facilitate the overlaying of the soybean physical map with the Medicago truncatula physical map, will aid in the comparative alignment of the soybean physical map with Arabidopsis sequence, and will provide much needed sequence for the development of molecular markers.…”

Section: Future Strategies For Soybean Genomicsmentioning

confidence: 99%

National Science Foundation-Sponsored Workshop Report. Draft Plan for Soybean Genomics

et al. 2004

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Recent efforts to coordinate and define a research strategy for soybean (Glycine max) genomics began with the establishment of a Soybean Genetics Executive Committee, which will serve as a communication focal point between the soybean research community and granting agencies. Secondly, a workshop was held to define a strategy to incorporate existing tools into a framework for advancing soybean genomics research. This workshop identified and ranked research priorities essential to making more informed decisions as to how to proceed with large scale sequencing and other genomics efforts. Most critical among these was the need to finalize a physical map and to obtain a better understanding of genome microstructure. Addressing these research needs will require pilot work on new technologies to demonstrate an ability to discriminate between recently duplicated regions in the soybean genome and pilot projects to analyze an adequate amount of random genome sequence to identify and catalog common repeats. The development of additional markers, reverse genetics tools, and bioinformatics is also necessary. Successful implementation of these goals will require close coordination among various working groups.

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“…Additionally, genecontaining BACs had been identified in the library HVVMRXALLhA and rearrayed for fingerprinting (The International Barley Genome Sequencing Consortium, 2012). We analyzed 690,912 barley BAC clones from these six libraries by high-information content fingerprinting (HICF; Luo et al, 2003; Table I). Fingerprint profiles were checked for plate-wide, neighboring, or chloroplast contamination as well as for clones containing more than 250 or less than 30 fragments.…”

Section: Assembly Of the Physical Mapmentioning

confidence: 99%

“…These had been either constructed by partial enzymatic fragmentation of high-M r DNA with the restriction endonucleases HindIII, EcoRI, or MboI or after mechanical fragmentation and blunt-end ligation. Plasmid DNA was isolated from a total of 690,912 BAC clones as described previously and was subjected to HICF according to published procedures (Luo et al, 2003). Peak areas, peak heights, and fragment sizes of each BAC fingerprint profile were collected by the Applied Biosystems 3730xl data collection program.…”

Section: Hicf and Automatic Contig Assemblymentioning

confidence: 99%

A Sequence-Ready Physical Map of Barley Anchored Genetically by Two Million Single-Nucleotide Polymorphisms

et al. 2013

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Barley (Hordeum vulgare) is an important cereal crop and a model species for Triticeae genomics. To lay the foundation for hierarchical map-based sequencing, a genome-wide physical map of its large and complex 5.1 billion-bp genome was constructed by high-information content fingerprinting of almost 600,000 bacterial artificial chromosomes representing 14-fold haploid genome coverage. The resultant physical map comprises 9,265 contigs with a cumulative size of 4.9 Gb representing 96% of the physical length of the barley genome. The reliability of the map was verified through extensive genetic marker information and the analysis of topological networks of clone overlaps. A minimum tiling path of 66,772 minimally overlapping clones was defined that will serve as a template for hierarchical clone-by-clone map-based shotgun sequencing. We integrated whole-genome shotgun sequence data from the individuals of two mapping populations with published bacterial artificial chromosome survey sequence information to genetically anchor the physical map. This novel approach in combination with the comprehensive whole-genome shotgun sequence data sets allowed us to independently validate and improve a previously reported physical and genetic framework. The resources developed in this study will underpin fine-mapping and cloning of agronomically important genes and the assembly of a draft genome sequence.

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High-throughput fingerprinting of bacterial artificial chromosomes using the snapshot labeling kit and sizing of restriction fragments by capillary electrophoresis

Cited by 235 publications

References 14 publications

A physical, genetic and functional sequence assembly of the barley genome

A physical, genetic and functional sequence assembly of the barley genome

National Science Foundation-Sponsored Workshop Report. Draft Plan for Soybean Genomics

A Sequence-Ready Physical Map of Barley Anchored Genetically by Two Million Single-Nucleotide Polymorphisms

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